MERFISH Report

1. Overview

1.1 Sample Information

A brief sample information is generated from the submission table for the following analysis.

Expt Sample Genotype DataPath Region
1 011_GFP GFP Z:/Lab/MERFISH_Imaging_data/202402181603_20240218Julio011n009VZG191m500x01_VMSC00101 region_1
1 009_GFP-cre GFPcre Z:/Lab/MERFISH_Imaging_data/202402181603_20240218Julio011n009VZG191m500x01_VMSC00101 region_0
2 008_GFP-cre GFPcre Z:/Lab/MERFISH_Imaging_data/202402181602_20240218Julio724n008VZG191m500x02_VMSC05201 region_1
2 724_GFP GFP Z:/Lab/MERFISH_Imaging_data/202402181602_20240218Julio724n008VZG191m500x02_VMSC05201 region_0

1.2 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

2. Data Processing & Analysis

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.

2.2 Batch Effect & Dimension Reduction

We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.

Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.

3. Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3). Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample.

3.1 Cell Annotation (Low resolution)

3.2 Cell Annotation (High resolution)

3.3 Finalized cell type Umap

3.4 Spatial cell type (All)

3.5 Spatial cell type (Glut)

3.6 Spatial cell type (Non-Neuron)

3.7 Cell Type Qualification Analysis

Cell Type Count
cell_type_3 008_GFP-cre 009_GFP-cre 011_GFP 724_GFP Total
Astrocyte 3360 5338 7692 2803 19193
CA1 Glut 159 114 682 249 1204
CA3 Glut 490 414 582 395 1881
CB Neuron 1699 1292 1615 1723 6329
CHOR 147 153 201 225 726
DG Glut 342 25 1006 520 1893
Endothelial 2581 4186 5469 3467 15703
L2/3 IT Glut 1881 1548 2495 1279 7203
L4/5 IT Glut 2846 2454 3958 2825 12083
L5 ET Glut 404 252 538 396 1590
L6 CT Glut 1241 1050 1848 1404 5543
L6 IT Glut 1197 945 1268 845 4255
L6b Glut 412 288 503 384 1587
MY/MB/P/HY Neuron 7853 5372 6831 6434 26490
Microglia 2447 5757 2869 1238 12311
OPC 1545 2180 1827 1182 6734
Oligo 5533 7950 11234 8013 32730
Pericyte 980 1634 2215 1495 6324
Pvalb GABA 609 500 792 615 2516
STR Neuron 5084 4283 6245 4599 20211
SUB Glut 56 12 82 64 214
Sst GABA 708 539 731 552 2530
TH Neuron 767 767 1344 1020 3898
VLMC 425 862 1441 427 3155
Vip/Lamp5/Sncg GABA 476 461 818 410 2165
Total 43242 48376 64286 42564 198468

3.8 Cell Type Proportion Analysis

Based on the quantification of individual cell types, we are capable to compare the differences in cell numbers between various samples and genotypes. The proportion of each cell type is calculated by dividing the count of that specific cell type by the total cell count. The results are then visualized in a bar plot.

Notably, B cells, mast cells, and T cells show an obvious increase in tumor samples.

4. Gene differentiation (GFP-Cre v.s. GFP)

Here, we use Wilcoxon rank-sum test to compute gene differential expression (DE). P value are adjusted using Benjamini–Hochberg procedure. The statistical significance was cut-off by log2(Fold Change) > 2 or log2(Fold Change) < -2 and p_value < 0.05.

The result are visualized via Volcano plot: a type of scatterplot that shows statistical significance (P value) versus magnitude of change (fold change).

The comparison is between GFP-Cre and GFP samples. A positive fold change means higher expression in the tumor group.

4.1 Astrocyte

names scores logfoldchanges pvals pvals_adj
Cd74 12.086074 3.327578 0.0000000 0.0000000
Cxcl10 4.140793 2.956832 0.0000346 0.0001602
Clec7a 2.791419 2.463387 0.0052477 0.0191524
C3 7.554973 2.390071 0.0000000 0.0000000
Lcn2 3.263298 2.218016 0.0011012 0.0044766
Serpina3n 15.881881 1.702190 0.0000000 0.0000000
Npas1 3.074245 1.395589 0.0021104 0.0081168
Ctss 11.239871 1.059485 0.0000000 0.0000000
Bcan -42.966170 -1.050833 0.0000000 0.0000000
Cspg5 -30.998905 -1.033761 0.0000000 0.0000000
Icam1 4.698708 1.012976 0.0000026 0.0000135

4.2 CA1 Glut

names scores logfoldchanges pvals pvals_adj
Drd5 -6.191965 -3.230274 0.0000000 0.0000000
Lratd2 -4.054375 -3.133397 0.0000503 0.0002513
Lct -3.898989 -3.115809 0.0000966 0.0004600
Kcnh7 -8.710794 -2.806653 0.0000000 0.0000000
Bcan -12.180642 -2.713535 0.0000000 0.0000000
Wfs1 -15.609615 -2.604273 0.0000000 0.0000000
Arc -13.357514 -2.600173 0.0000000 0.0000000
Gm2115 -12.618988 -2.565489 0.0000000 0.0000000
Gpr63 -6.843199 -2.557320 0.0000000 0.0000000
Egr4 -8.029078 -2.446723 0.0000000 0.0000000
Lamp5 -4.905334 -2.406227 0.0000009 0.0000053
Epha10 -7.344985 -2.288014 0.0000000 0.0000000
Scn4b -5.658706 -2.250183 0.0000000 0.0000001
Col11a1 -4.169776 -2.233136 0.0000305 0.0001588
Itga7 -5.319431 -2.232415 0.0000001 0.0000007
Gabra1 -9.056701 -2.164254 0.0000000 0.0000000
Epha7 -10.708636 -2.157751 0.0000000 0.0000000
Trib2 4.592781 2.153502 0.0000044 0.0000238
Egr2 -2.749730 -2.129920 0.0059644 0.0202872
Col6a1 10.558397 2.123981 0.0000000 0.0000000
Neurod6 -10.620948 -2.088480 0.0000000 0.0000000
Nrg2 -4.106236 -2.059862 0.0000402 0.0002052
Plagl1 12.469936 2.047164 0.0000000 0.0000000
Kcnd2 -12.667880 -2.041409 0.0000000 0.0000000
Egr1 -12.270212 -2.017097 0.0000000 0.0000000
Htr1a -8.327378 -2.003451 0.0000000 0.0000000
Enpp2 -3.970348 -1.972346 0.0000718 0.0003484
Wnt2 -3.372658 -1.919400 0.0007445 0.0030511
Dkk3 -11.076118 -1.886895 0.0000000 0.0000000
Ndst4 -3.684617 -1.776482 0.0002290 0.0010411
Bcl11b -10.986549 -1.757803 0.0000000 0.0000000
Hs3st1 -3.228753 -1.736715 0.0012433 0.0047455
Hpca -11.887192 -1.693197 0.0000000 0.0000000
Ntsr1 -2.846129 -1.673668 0.0044254 0.0154735
Grp 6.490464 1.666033 0.0000000 0.0000000
Adgrl2 -9.457041 -1.659944 0.0000000 0.0000000
Lmo1 -5.903759 -1.656389 0.0000000 0.0000000
Nr4a1 -9.498807 -1.634760 0.0000000 0.0000000
Grin2a -15.506289 -1.630166 0.0000000 0.0000000
Meis2 -4.634052 -1.617793 0.0000036 0.0000199
Cckbr -2.993992 -1.573156 0.0027535 0.0099048
Camk2a -15.047456 -1.566388 0.0000000 0.0000000
Npy1r -2.551193 -1.559665 0.0107355 0.0343549
Gpr37 -3.572779 -1.553403 0.0003532 0.0015095
Car4 -3.364344 -1.530297 0.0007673 0.0031189
Hrh3 7.125565 1.521176 0.0000000 0.0000000
Pkp2 -8.441889 -1.518617 0.0000000 0.0000000
Nr2f2 9.476934 1.445323 0.0000000 0.0000000
Sox8 -2.703016 -1.433652 0.0068714 0.0230582
Tbr1 -2.569602 -1.406019 0.0101815 0.0332730
Kcnab1 -14.668692 -1.405700 0.0000000 0.0000000
Nr4a2 -9.212976 -1.399824 0.0000000 0.0000000
Ctsb -9.975059 -1.390653 0.0000000 0.0000000
Adrb1 -6.541533 -1.384369 0.0000000 0.0000000
Osr1 2.776255 1.378816 0.0054989 0.0188319
Fam131a -14.343471 -1.359657 0.0000000 0.0000000
Bcl6 -9.020180 -1.350236 0.0000000 0.0000000
Cx3cl1 -14.619305 -1.308419 0.0000000 0.0000000
Grm1 -2.915805 -1.296162 0.0035477 0.0124920
Crhr1 -6.547669 -1.293980 0.0000000 0.0000000
Plp1 -9.618266 -1.258812 0.0000000 0.0000000
Ptk2b -14.057443 -1.256055 0.0000000 0.0000000
Robo1 -8.604202 -1.254897 0.0000000 0.0000000
Nectin3 -2.918675 -1.254360 0.0035152 0.0124653
Myh11 2.730728 1.242063 0.0063195 0.0213496
Gria3 -10.072248 -1.234077 0.0000000 0.0000000
Gria1 -12.679262 -1.230100 0.0000000 0.0000000
Id4 -3.177882 -1.219708 0.0014836 0.0054946
Rbfox3 -12.419758 -1.203092 0.0000000 0.0000000
Plekhg1 -4.985698 -1.193509 0.0000006 0.0000036
Cdh12 -3.025267 -1.192861 0.0024841 0.0090005
Brinp1 -9.969714 -1.179770 0.0000000 0.0000000
Gfap 7.630815 1.176230 0.0000000 0.0000000
Mapk1 -5.205019 -1.173542 0.0000002 0.0000012
Gpc3 -2.674611 -1.152955 0.0074816 0.0247735
Sorl1 -10.104910 -1.133160 0.0000000 0.0000000
Pdzrn4 -4.074763 -1.114685 0.0000461 0.0002326
Grin2b -12.796247 -1.098387 0.0000000 0.0000000
Adam10 -4.024287 -1.093711 0.0000571 0.0002829
Car12 -4.311800 -1.086797 0.0000162 0.0000861
Gria2 -10.899653 -1.074424 0.0000000 0.0000000
Pcdh9 -8.576984 -1.067766 0.0000000 0.0000000
Prkce -7.554013 -1.042431 0.0000000 0.0000000
Cck -10.265838 -1.029759 0.0000000 0.0000000
Crtac1 8.106077 1.027262 0.0000000 0.0000000
Smad3 -6.919704 -1.020970 0.0000000 0.0000000
Tnik -3.587724 -1.013020 0.0003336 0.0014378
Dclk3 -6.011837 -1.005108 0.0000000 0.0000000

4.3 CA3 Glut

names scores logfoldchanges pvals pvals_adj
Sema5b -9.963718 -2.998168 0.0000000 0.0000000
Scn4b -5.253923 -2.418384 0.0000001 0.0000007
Iyd -6.936011 -2.402789 0.0000000 0.0000000
Trib2 9.562335 2.392363 0.0000000 0.0000000
Prkcd -8.414603 -2.260338 0.0000000 0.0000000
Car4 -10.588140 -2.221318 0.0000000 0.0000000
Itga7 -8.698009 -2.178149 0.0000000 0.0000000
Npy 7.757045 1.963502 0.0000000 0.0000000
Cckbr -6.051846 -1.935948 0.0000000 0.0000000
Bcan -10.321513 -1.904332 0.0000000 0.0000000
Neurod6 -10.836412 -1.840740 0.0000000 0.0000000
Ly6g6e 3.509724 1.813584 0.0004486 0.0016136
Grm2 7.685248 1.810627 0.0000000 0.0000000
Npy2r -14.434289 -1.653863 0.0000000 0.0000000
Robo1 -13.289022 -1.551422 0.0000000 0.0000000
Nr4a2 -8.138291 -1.494950 0.0000000 0.0000000
Ntf3 -2.654873 -1.478802 0.0079338 0.0234729
Nectin3 -8.215781 -1.472096 0.0000000 0.0000000
Grp 7.510216 1.436703 0.0000000 0.0000000
Nos1 -8.529648 -1.393604 0.0000000 0.0000000
Cdh12 -4.421758 -1.388731 0.0000098 0.0000415
Fibcd1 8.154010 1.388414 0.0000000 0.0000000
Enpp2 -5.151538 -1.367420 0.0000003 0.0000012
Mmp9 -2.457155 -1.357622 0.0140042 0.0393377
Dcn -3.888931 -1.322337 0.0001007 0.0003933
Id4 -4.314869 -1.317898 0.0000160 0.0000671
Rph3a -9.515093 -1.307395 0.0000000 0.0000000
Crhr1 -9.526181 -1.294305 0.0000000 0.0000000
Plekhg1 -7.455498 -1.289077 0.0000000 0.0000000
Plcxd2 -5.660659 -1.284401 0.0000000 0.0000001
Ngb -2.922178 -1.265845 0.0034759 0.0112127
Cd83 -2.539063 -1.262204 0.0111150 0.0319396
Gpr63 -4.909085 -1.249100 0.0000009 0.0000042
Tcf7l2 -2.758872 -1.247907 0.0058001 0.0179529
Serpina3n 9.481787 1.241485 0.0000000 0.0000000
Penk 6.853083 1.227823 0.0000000 0.0000000
Kit -9.849012 -1.195954 0.0000000 0.0000000
Npy1r -4.045355 -1.154759 0.0000522 0.0002073
Camk4 -12.986540 -1.153570 0.0000000 0.0000000
Dclk3 6.902831 1.146178 0.0000000 0.0000000
Hs3st1 -2.995930 -1.136096 0.0027361 0.0090003
Egr1 -8.938679 -1.132204 0.0000000 0.0000000
Plxna1 -12.746381 -1.129517 0.0000000 0.0000000
Epha7 -8.916927 -1.129469 0.0000000 0.0000000
Gm2115 -2.732193 -1.122267 0.0062914 0.0192989
Mfsd2a 5.828553 1.104306 0.0000000 0.0000000
Gfap 12.501422 1.095731 0.0000000 0.0000000
Dkk3 -8.220496 -1.095488 0.0000000 0.0000000
Cd74 2.627344 1.072469 0.0086054 0.0253101
Arc -6.742881 -1.072258 0.0000000 0.0000000
Npnt 3.079962 1.065957 0.0020703 0.0069942
Esrrg -2.812529 -1.049165 0.0049154 0.0154571
Syndig1l -2.450783 -1.020547 0.0142546 0.0398173
Ntng1 -3.046867 -1.014938 0.0023124 0.0077080
Adrb1 -4.206749 -1.007670 0.0000259 0.0001062
Adamts15 -3.706550 -1.007478 0.0002101 0.0007724
Tbr1 -3.876993 -1.006026 0.0001058 0.0004068

4.4 CB Neuron

names scores logfoldchanges pvals pvals_adj
Fos -9.153584 -1.148150 0 0e+00
Vgf -5.476257 -1.059721 0 5e-07
Nr4a1 -9.550865 -1.049225 0 0e+00

4.5 CHOR

names scores logfoldchanges pvals pvals_adj
Spp1 4.606217 3.174009 0.0000041 0.0006834
Ctss 6.506277 2.558002 0.0000000 0.0000000
Cd74 5.074853 1.410833 0.0000004 0.0000969
Vtn -3.130588 -1.229544 0.0017446 0.0459096

4.6 DG Glut

names scores logfoldchanges pvals pvals_adj
Car4 -5.954676 -4.612063 0.0000000 0.0000000
Iyd -2.888605 -3.897872 0.0038696 0.0132519
Crebbp -3.138983 -3.448560 0.0016954 0.0060984
Sema5b -8.070182 -3.381921 0.0000000 0.0000000
Prox1 -11.451460 -3.376683 0.0000000 0.0000000
Col6a1 15.069502 3.340746 0.0000000 0.0000000
Pdyn -7.780768 -3.314382 0.0000000 0.0000000
Npy2r -12.682557 -3.251736 0.0000000 0.0000000
Adarb2 -3.165893 -3.200292 0.0015461 0.0056426
Grm1 -7.125413 -3.194595 0.0000000 0.0000000
Itga7 -9.832137 -3.168897 0.0000000 0.0000000
Cdh12 -4.002225 -3.060751 0.0000627 0.0002615
Drd5 -6.111296 -3.035839 0.0000000 0.0000000
Gng2 -9.008463 -2.926049 0.0000000 0.0000000
Cd74 4.023231 2.919960 0.0000574 0.0002432
Chrna7 -9.060155 -2.903636 0.0000000 0.0000000
Negr1 -5.343089 -2.808587 0.0000001 0.0000005
Cspg5 -11.802776 -2.747140 0.0000000 0.0000000
Prkce -16.241940 -2.742629 0.0000000 0.0000000
Ntng1 -6.836531 -2.740882 0.0000000 0.0000000
Sox8 -5.521832 -2.728541 0.0000000 0.0000002
Npy1r -7.011711 -2.691978 0.0000000 0.0000000
Rims1 -9.185610 -2.669787 0.0000000 0.0000000
Adrb1 -6.496010 -2.666402 0.0000000 0.0000000
Kcnd2 -14.632668 -2.638562 0.0000000 0.0000000
Epha10 -8.286418 -2.610015 0.0000000 0.0000000
Camk2a -22.759329 -2.600446 0.0000000 0.0000000
Camk2g -17.222553 -2.585930 0.0000000 0.0000000
Cdh9 -5.595223 -2.569636 0.0000000 0.0000001
Gabra1 -7.970254 -2.567054 0.0000000 0.0000000
Mapk1 -7.810337 -2.552455 0.0000000 0.0000000
Lratd2 -10.576093 -2.532518 0.0000000 0.0000000
Egr4 -3.345221 -2.521988 0.0008222 0.0031622
Lct -12.001356 -2.498596 0.0000000 0.0000000
Ctnnb1 -15.471447 -2.491804 0.0000000 0.0000000
Plcg2 -5.524385 -2.484487 0.0000000 0.0000002
Syt17 -14.850075 -2.463463 0.0000000 0.0000000
Nr4a2 -5.416001 -2.437834 0.0000001 0.0000003
Tbr1 -8.811000 -2.432638 0.0000000 0.0000000
Gpc3 -3.008848 -2.406959 0.0026224 0.0091692
Gria2 -20.482897 -2.381789 0.0000000 0.0000000
Nos1 -7.465934 -2.368460 0.0000000 0.0000000
Rasgrf2 -10.594121 -2.311158 0.0000000 0.0000000
Ntng2 -14.831568 -2.301035 0.0000000 0.0000000
Cck -11.339354 -2.295702 0.0000000 0.0000000
Mas1 -13.068602 -2.294961 0.0000000 0.0000000
Ctsb -11.517192 -2.286616 0.0000000 0.0000000
Ntf3 -4.548292 -2.199327 0.0000054 0.0000244
Bcl11b -14.791788 -2.170556 0.0000000 0.0000000
Lamp5 -3.021612 -2.160039 0.0025143 0.0088533
Gpr158 -11.423912 -2.128592 0.0000000 0.0000000
Sorl1 -15.302543 -2.111150 0.0000000 0.0000000
Kctd4 -7.967329 -2.090750 0.0000000 0.0000000
Nrg2 -12.488551 -2.050165 0.0000000 0.0000000
Smad3 -15.523778 -2.040720 0.0000000 0.0000000
Cpne6 -21.323004 -2.017199 0.0000000 0.0000000
Cacng5 -2.553455 -1.999802 0.0106660 0.0346299
Nr2f2 4.261006 1.981966 0.0000204 0.0000900
Ptk2b -23.221050 -1.943977 0.0000000 0.0000000
Tnik -4.131775 -1.921604 0.0000360 0.0001552
Myo5a -9.692004 -1.905438 0.0000000 0.0000000
Rph3a -18.126266 -1.885537 0.0000000 0.0000000
Gria1 -20.174604 -1.856521 0.0000000 0.0000000
Fam131a -20.078930 -1.853892 0.0000000 0.0000000
Csf1 -8.562962 -1.836201 0.0000000 0.0000000
Synpr -2.511388 -1.830895 0.0120257 0.0385440
Ndst4 -3.085163 -1.820293 0.0020344 0.0072657
Vgf 12.380434 1.812606 0.0000000 0.0000000
Grin2a -18.679565 -1.804108 0.0000000 0.0000000
Syp -20.636219 -1.792395 0.0000000 0.0000000
Lrpprc -7.629042 -1.779802 0.0000000 0.0000000
Kcnc1 -14.058948 -1.775951 0.0000000 0.0000000
Lmo1 -5.532681 -1.772336 0.0000000 0.0000002
Ctss 4.988901 1.747297 0.0000006 0.0000029
Pcdhgc5 -14.246465 -1.741296 0.0000000 0.0000000
Ngrn -3.153555 -1.720106 0.0016129 0.0058440
Gpr37 -3.770673 -1.713156 0.0001628 0.0006672
Car12 -9.476565 -1.705796 0.0000000 0.0000000
Pkp2 -8.785366 -1.700253 0.0000000 0.0000000
Cx3cl1 -17.965391 -1.698011 0.0000000 0.0000000
Bcan -3.362026 -1.681482 0.0007737 0.0029989
Eno2 -17.855467 -1.676016 0.0000000 0.0000000
Sox10 3.197749 1.653551 0.0013850 0.0051681
Hpca -17.464636 -1.642875 0.0000000 0.0000000
Npnt -9.217944 -1.608085 0.0000000 0.0000000
Stard8 -4.100930 -1.606739 0.0000411 0.0001759
Ntrk2 -3.773757 -1.592374 0.0001608 0.0006645
Dapk1 -13.117635 -1.588032 0.0000000 0.0000000
Htr1a -5.205083 -1.570749 0.0000002 0.0000010
Pcdh9 -12.586990 -1.565680 0.0000000 0.0000000
Neto1 -9.151893 -1.556741 0.0000000 0.0000000
Bace1 -3.078888 -1.522918 0.0020777 0.0073679
Npy 2.414386 1.495330 0.0157618 0.0495653
Fibcd1 -5.910163 -1.448798 0.0000000 0.0000000
Sstr3 -3.250877 -1.438732 0.0011505 0.0043579
Psen2 -4.228139 -1.432190 0.0000236 0.0001033
Adam10 -3.641654 -1.424411 0.0002709 0.0010582
Grm3 -3.724617 -1.418961 0.0001956 0.0007824
Robo1 -5.001026 -1.407868 0.0000006 0.0000027
Slc17a7 -16.818161 -1.402455 0.0000000 0.0000000
Bin1 -14.892460 -1.401940 0.0000000 0.0000000
Grb2 -8.933210 -1.398963 0.0000000 0.0000000
Tmem150a -4.775696 -1.375869 0.0000018 0.0000084
Gad1 -7.662386 -1.374605 0.0000000 0.0000000
Psen1 -6.392944 -1.371679 0.0000000 0.0000000
Slc29a1 -5.192851 -1.365064 0.0000002 0.0000010
Mink1 -15.699117 -1.352942 0.0000000 0.0000000
Pcdhgc3 -4.684437 -1.324283 0.0000028 0.0000130
Src -12.334910 -1.300029 0.0000000 0.0000000
Gria3 -10.233817 -1.297208 0.0000000 0.0000000
Map4k3 -4.719217 -1.295583 0.0000024 0.0000111
Pdgfa -7.075901 -1.294499 0.0000000 0.0000000
Fermt2 -3.209395 -1.291492 0.0013301 0.0050005
Bcl6 -9.176941 -1.289376 0.0000000 0.0000000
Grm2 -11.933922 -1.246578 0.0000000 0.0000000
Gfap 8.050611 1.215875 0.0000000 0.0000000
Epha7 -11.008564 -1.179198 0.0000000 0.0000000
Nptx1 -15.579086 -1.169732 0.0000000 0.0000000
Slc29a2 -2.533299 -1.115754 0.0112994 0.0364498
Pcdhac2 -5.335271 -1.081160 0.0000001 0.0000005
Grin2b -13.881853 -1.062299 0.0000000 0.0000000
Rbfox3 -13.661894 -1.057280 0.0000000 0.0000000
Gphn -6.575463 -1.003536 0.0000000 0.0000000
Plp1 -6.687304 -1.002527 0.0000000 0.0000000

4.7 Endothelial

names scores logfoldchanges pvals pvals_adj
Cd74 9.577570 2.585067 0.0000000 0.0000000
Serpina3n 3.748965 1.962930 0.0001776 0.0012683
C4b 5.126868 1.218350 0.0000003 0.0000031
Fos -3.957550 -1.149680 0.0000757 0.0005651
Gfap 18.504066 1.106034 0.0000000 0.0000000
Synpo2 -10.172818 -1.001326 0.0000000 0.0000000

4.8 L2_3 IT Glut

names scores logfoldchanges pvals pvals_adj
Fibcd1 -8.174534 -2.622705 0.0000000 0.0000000
Ndnf -2.873666 -1.840048 0.0040574 0.0099446
Egr4 -20.676815 -1.770479 0.0000000 0.0000000
Egr2 -15.297562 -1.753064 0.0000000 0.0000000
Fos -22.158278 -1.699495 0.0000000 0.0000000
Fosl2 -22.131536 -1.695000 0.0000000 0.0000000
Car4 -13.500947 -1.679523 0.0000000 0.0000000
Fosb -14.063915 -1.626696 0.0000000 0.0000000
Nr4a2 -11.575624 -1.533527 0.0000000 0.0000000
Adrb1 -29.606792 -1.473771 0.0000000 0.0000000
Egr1 -34.335995 -1.441938 0.0000000 0.0000000
Nr4a1 -30.301668 -1.434474 0.0000000 0.0000000
Sema5b -9.691622 -1.390324 0.0000000 0.0000000
Npnt -13.856658 -1.354121 0.0000000 0.0000000
Cspg5 -28.605438 -1.347954 0.0000000 0.0000000
Cd74 6.349783 1.346901 0.0000000 0.0000000
Ptpru -13.878231 -1.325718 0.0000000 0.0000000
Crhr1 -29.079260 -1.278748 0.0000000 0.0000000
Mgp -3.036500 -1.232444 0.0023934 0.0060440
Scn4b -13.329892 -1.229025 0.0000000 0.0000000
Nectin3 -15.859935 -1.226602 0.0000000 0.0000000
Rph3a -30.927746 -1.216501 0.0000000 0.0000000
Fezf2 -2.943514 -1.213592 0.0032451 0.0080324
Lamp5 -25.432514 -1.201549 0.0000000 0.0000000
Cx3cl1 -37.528553 -1.180060 0.0000000 0.0000000
Camk4 -31.443071 -1.172730 0.0000000 0.0000000
Jam2 -2.697098 -1.157315 0.0069947 0.0168953
Apoe -29.598629 -1.145100 0.0000000 0.0000000
Bcan -13.610049 -1.139868 0.0000000 0.0000000
Otof -14.906362 -1.130868 0.0000000 0.0000000
Ppp1r1b 28.204140 1.130331 0.0000000 0.0000000
Grm2 -20.895922 -1.124576 0.0000000 0.0000000
Ngb -4.389131 -1.111987 0.0000114 0.0000343
Ddit4l -3.705112 -1.105471 0.0002113 0.0005869
Lrrc55 -15.108859 -1.103727 0.0000000 0.0000000
Grp -3.910503 -1.098897 0.0000921 0.0002647
Stard8 -22.458380 -1.093667 0.0000000 0.0000000
Sox8 -13.469996 -1.089075 0.0000000 0.0000000
Gfap 20.074620 1.086906 0.0000000 0.0000000
Mas1 -17.865356 -1.086671 0.0000000 0.0000000
Penk -13.268831 -1.064893 0.0000000 0.0000000
Rspo1 -5.410357 -1.062304 0.0000001 0.0000002
Lratd2 -3.000570 -1.048828 0.0026948 0.0067369
Oxgr1 -4.946007 -1.038561 0.0000008 0.0000025

4.9 L4_5 IT Glut

names scores logfoldchanges pvals pvals_adj
Cd74 13.180964 3.145334 0.0000000 0.0000000
Egr2 -15.693312 -1.763540 0.0000000 0.0000000
Cxcl10 3.319119 1.525908 0.0009030 0.0029705
Egr4 -18.764074 -1.518028 0.0000000 0.0000000
Fosb -13.508392 -1.514867 0.0000000 0.0000000
Bcan -14.650078 -1.369449 0.0000000 0.0000000
Gfap 20.850578 1.327615 0.0000000 0.0000000
Igf2 -4.037504 -1.297898 0.0000540 0.0001957
Cspg5 -30.988180 -1.239828 0.0000000 0.0000000
Serpina3n 4.594737 1.233951 0.0000043 0.0000179
Fos -22.736520 -1.230804 0.0000000 0.0000000
Adrb1 -22.953900 -1.183014 0.0000000 0.0000000
Clec7a 2.514453 1.172788 0.0119217 0.0331159
Sst -13.747972 -1.168542 0.0000000 0.0000000
Scn4b -16.260290 -1.160662 0.0000000 0.0000000
Sox8 -10.863413 -1.155441 0.0000000 0.0000000
Fosl2 -14.978842 -1.137228 0.0000000 0.0000000
Htr1a -8.065847 -1.121700 0.0000000 0.0000000
Apoe -29.738697 -1.105550 0.0000000 0.0000000
Rph3a -34.846806 -1.077260 0.0000000 0.0000000
C4b 3.144409 1.023812 0.0016642 0.0053001
Egr1 -30.680056 -1.013146 0.0000000 0.0000000
Grm4 -15.561079 -1.009871 0.0000000 0.0000000

4.10 L5 ET Glut

names scores logfoldchanges pvals pvals_adj
Cd74 6.588143 3.480968 0.0000000 0.0000000
Egr2 -3.961940 -1.917788 0.0000743 0.0003442
Egr4 -11.947008 -1.740308 0.0000000 0.0000000
Fosb -5.537108 -1.479007 0.0000000 0.0000002
Htr1a -3.608506 -1.420444 0.0003080 0.0013049
Sst -10.027505 -1.412893 0.0000000 0.0000000
Cspg5 -13.398189 -1.326896 0.0000000 0.0000000
Pcdh11x -3.852487 -1.260020 0.0001169 0.0005220
Egr1 -13.578428 -1.251176 0.0000000 0.0000000
Adrb1 -10.681449 -1.250625 0.0000000 0.0000000
Fos -8.049476 -1.181501 0.0000000 0.0000000
Gfap 7.423714 1.173134 0.0000000 0.0000000
Lrrc55 -2.823252 -1.159461 0.0047539 0.0178719
Apoe -13.366623 -1.092326 0.0000000 0.0000000
Tpbg -3.125981 -1.067182 0.0017721 0.0070323
Nr4a2 -4.620321 -1.047722 0.0000038 0.0000202
Enpp2 -6.522738 -1.047069 0.0000000 0.0000000
Ntsr1 -2.649393 -1.033771 0.0080637 0.0289913
Cx3cl1 -13.574212 -1.022074 0.0000000 0.0000000
Kcnab1 -10.200034 -1.016279 0.0000000 0.0000000

4.11 L6 CT Glut

names scores logfoldchanges pvals pvals_adj
Cd74 11.045413 3.828277 0.0000000 0.0000000
Egr2 -11.265487 -2.128186 0.0000000 0.0000000
Egr4 -12.481452 -1.869583 0.0000000 0.0000000
Fos -20.459060 -1.783920 0.0000000 0.0000000
Fosb -6.778194 -1.690296 0.0000000 0.0000000
Grp -7.681380 -1.651657 0.0000000 0.0000000
Sema5b -16.287370 -1.626038 0.0000000 0.0000000
Htr1a -7.330582 -1.623997 0.0000000 0.0000000
Fosl2 -10.674314 -1.614164 0.0000000 0.0000000
Nr4a1 -29.766352 -1.520325 0.0000000 0.0000000
Sox8 -17.210140 -1.443844 0.0000000 0.0000000
Egr1 -28.885315 -1.207918 0.0000000 0.0000000
Nr4a2 -10.304528 -1.198852 0.0000000 0.0000000
Cspg5 -20.882948 -1.180324 0.0000000 0.0000000
Cxcl10 2.554330 1.151787 0.0106393 0.0366871
Serpina3n 3.353295 1.132084 0.0007986 0.0032462
Cx3cl1 -29.568316 -1.033014 0.0000000 0.0000000
Adrb1 -12.748731 -1.032174 0.0000000 0.0000000

4.12 L6 IT Glut

names scores logfoldchanges pvals pvals_adj
Cd74 6.659259 2.557009 0.0000000 0.0000000
Fosl2 -15.437291 -1.801963 0.0000000 0.0000000
Egr2 -5.813492 -1.614173 0.0000000 0.0000000
Penk -15.342633 -1.560274 0.0000000 0.0000000
Fosb -8.443142 -1.501059 0.0000000 0.0000000
Egr4 -10.693886 -1.475045 0.0000000 0.0000000
Ptpru -22.552866 -1.448234 0.0000000 0.0000000
Sox8 -15.520917 -1.412241 0.0000000 0.0000000
Adrb1 -20.434456 -1.394861 0.0000000 0.0000000
Htr1a -9.371473 -1.351679 0.0000000 0.0000000
Egr1 -25.639118 -1.316748 0.0000000 0.0000000
Fos -12.646792 -1.305286 0.0000000 0.0000000
Cspg5 -22.620780 -1.282444 0.0000000 0.0000000
Tpbg -5.211852 -1.262050 0.0000002 0.0000007
Mog -5.298135 -1.234448 0.0000001 0.0000005
Stard8 -10.588483 -1.231473 0.0000000 0.0000000
Nr4a1 -20.973999 -1.228160 0.0000000 0.0000000
Cldn11 -6.247221 -1.204305 0.0000000 0.0000000
Syt6 7.852458 1.193932 0.0000000 0.0000000
Sema5b -16.887383 -1.185215 0.0000000 0.0000000
Crhr1 -18.822767 -1.138837 0.0000000 0.0000000
Cckbr -21.306192 -1.120681 0.0000000 0.0000000
Enpp2 -13.248084 -1.111644 0.0000000 0.0000000
Cx3cl1 -26.957289 -1.095771 0.0000000 0.0000000
Rph3a -23.197723 -1.056088 0.0000000 0.0000000
Mas1 -11.243724 -1.014174 0.0000000 0.0000000
Cxcr4 3.077891 1.004127 0.0020847 0.0061678

4.13 L6b Glut

names scores logfoldchanges pvals pvals_adj
Cd74 5.714800 4.052389 0.0000000 0.0000001
Grp -4.308826 -1.418620 0.0000164 0.0001039
Bcan -5.311912 -1.229256 0.0000001 0.0000010
Cspg5 -11.514272 -1.153825 0.0000000 0.0000000
Adrb1 -5.293157 -1.058681 0.0000001 0.0000011
Lamp5 -3.121837 -1.057681 0.0017973 0.0097677
Tpbg -7.130207 -1.042298 0.0000000 0.0000000
Egr1 -10.115523 -1.035635 0.0000000 0.0000000
Cx3cl1 -15.160847 -1.002740 0.0000000 0.0000000

4.14 Microglia

names scores logfoldchanges pvals pvals_adj
Cd74 63.946007 4.973553 0.0000000 0.0000000
Cst7 24.697985 4.365547 0.0000000 0.0000000
C3 29.547565 4.028767 0.0000000 0.0000000
Cxcl10 8.001764 3.791353 0.0000000 0.0000000
Itgal 22.626020 3.734685 0.0000000 0.0000000
Lgals3 20.181517 3.703766 0.0000000 0.0000000
Spp1 21.749884 3.572593 0.0000000 0.0000000
Clec7a 16.080172 3.559483 0.0000000 0.0000000
C4b 37.264393 3.310130 0.0000000 0.0000000
Itgax 25.150688 2.782841 0.0000000 0.0000000
Xdh 21.722470 2.764679 0.0000000 0.0000000
Serpina3n 8.792327 2.612850 0.0000000 0.0000000
Tmem119 -54.498180 -2.413195 0.0000000 0.0000000
Cx3cr1 -55.075550 -2.339749 0.0000000 0.0000000
Gpc3 17.427013 2.171520 0.0000000 0.0000000
Cxcr4 6.154465 2.126732 0.0000000 0.0000000
Anpep 3.850223 2.110441 0.0001180 0.0003334
Cxcl2 13.279420 2.108510 0.0000000 0.0000000
Cd8a 5.297342 2.096031 0.0000001 0.0000004
Selplg -52.013844 -2.039347 0.0000000 0.0000000
Hpca -22.053387 -1.969876 0.0000000 0.0000000
Neu4 8.290473 1.952566 0.0000000 0.0000000
P2ry12 -34.855510 -1.926756 0.0000000 0.0000000
Egr4 -3.697687 -1.902346 0.0002176 0.0005977
Rph3a -26.152880 -1.892608 0.0000000 0.0000000
Siglech -40.673912 -1.855954 0.0000000 0.0000000
Cd4 3.901264 1.807051 0.0000957 0.0002734
Syp -27.992123 -1.803238 0.0000000 0.0000000
Gjb1 -5.976529 -1.786283 0.0000000 0.0000000
Bcan -16.760900 -1.758267 0.0000000 0.0000000
Grin2c -4.877934 -1.752813 0.0000011 0.0000034
Adrb1 -15.016638 -1.710413 0.0000000 0.0000000
Mog -7.923509 -1.710356 0.0000000 0.0000000
Fmo1 7.542876 1.706857 0.0000000 0.0000000
Lpl 4.196773 1.696768 0.0000271 0.0000796
Lcn2 2.791243 1.696106 0.0052506 0.0119877
Ddit3 22.460218 1.688921 0.0000000 0.0000000
Csf1r -47.201733 -1.687757 0.0000000 0.0000000
Cspg5 -15.670618 -1.681289 0.0000000 0.0000000
Gm2115 -3.509078 -1.680019 0.0004497 0.0011649
Cplx1 -29.083132 -1.675126 0.0000000 0.0000000
Camk2a -28.531832 -1.670738 0.0000000 0.0000000
Grin2b -13.318376 -1.661097 0.0000000 0.0000000
Scn4b -10.303435 -1.623348 0.0000000 0.0000000
Opalin -3.478325 -1.607014 0.0005046 0.0013004
Apoc1 2.682868 1.605342 0.0072994 0.0160779
Htr5a -2.313667 -1.601304 0.0206860 0.0425638
Syn1 -21.841890 -1.597705 0.0000000 0.0000000
Ly9 23.592302 1.596093 0.0000000 0.0000000
Neto1 -7.016478 -1.586585 0.0000000 0.0000000
Nefm -18.520222 -1.584442 0.0000000 0.0000000
Fam131a -19.516308 -1.580831 0.0000000 0.0000000
Id4 -7.511149 -1.577027 0.0000000 0.0000000
Kcnab1 -11.773004 -1.574934 0.0000000 0.0000000
Dlg4 -33.241410 -1.527379 0.0000000 0.0000000
Dnm1 -22.177908 -1.526562 0.0000000 0.0000000
Csf1 19.762161 1.511753 0.0000000 0.0000000
Slc32a1 -9.173188 -1.511452 0.0000000 0.0000000
Ppp1r3g -2.459668 -1.509429 0.0139065 0.0297148
Tnf 7.599371 1.509385 0.0000000 0.0000000
Eno2 -23.115350 -1.505098 0.0000000 0.0000000
Agt -7.149469 -1.494736 0.0000000 0.0000000
Tpbg -2.783541 -1.484553 0.0053769 0.0122203
Sox8 -7.911628 -1.481774 0.0000000 0.0000000
Slc7a10 -4.916309 -1.464087 0.0000009 0.0000028
Grin1 -19.321404 -1.462685 0.0000000 0.0000000
Mapt -21.850910 -1.456870 0.0000000 0.0000000
Grin2a -11.462131 -1.451628 0.0000000 0.0000000
S100b -13.454475 -1.440448 0.0000000 0.0000000
Cxcl14 -7.527935 -1.438474 0.0000000 0.0000000
Gabra1 -6.405670 -1.436034 0.0000000 0.0000000
Dkk3 -13.380318 -1.415208 0.0000000 0.0000000
Foxp2 -2.643956 -1.413301 0.0081943 0.0179700
Grm2 -3.341079 -1.393014 0.0008345 0.0020454
Atf3 11.670850 1.390785 0.0000000 0.0000000
Negr1 -3.382149 -1.388690 0.0007192 0.0017980
Grm3 -12.670980 -1.384276 0.0000000 0.0000000
Lamp5 -4.626317 -1.378511 0.0000037 0.0000113
Grm4 -3.739117 -1.378497 0.0001847 0.0005130
Cd14 -20.866608 -1.378410 0.0000000 0.0000000
Six3 -3.582945 -1.376206 0.0003397 0.0008988
Meis2 -8.014439 -1.374740 0.0000000 0.0000000
Pcdh9 -12.228945 -1.370368 0.0000000 0.0000000
Rgs5 -3.580261 -1.361154 0.0003433 0.0009033
Syngap1 -20.967163 -1.357107 0.0000000 0.0000000
Rbfox3 -15.165191 -1.348417 0.0000000 0.0000000
Gria2 -13.748306 -1.348030 0.0000000 0.0000000
Mfsd2a -3.649040 -1.346155 0.0002632 0.0007076
Epha10 -2.637206 -1.335845 0.0083592 0.0182515
Penk -7.827449 -1.334967 0.0000000 0.0000000
Ecscr -13.241029 -1.331579 0.0000000 0.0000000
Rgs12 15.605325 1.330034 0.0000000 0.0000000
Gpr37 -4.209537 -1.326365 0.0000256 0.0000757
Cckbr -3.652627 -1.323199 0.0002596 0.0007015
Rasgrf2 -4.842848 -1.322461 0.0000013 0.0000040
Bin1 -37.857285 -1.315697 0.0000000 0.0000000
Elfn1 -3.730522 -1.308409 0.0001911 0.0005279
Kcnd2 -6.114942 -1.302207 0.0000000 0.0000000
Lrrc55 -2.425841 -1.292904 0.0152730 0.0323580
Syt17 -2.455358 -1.286476 0.0140744 0.0299456
Nrg3 -5.688522 -1.282046 0.0000000 0.0000000
Cldn11 -5.734639 -1.281896 0.0000000 0.0000000
Ppp1r1b -13.126994 -1.276925 0.0000000 0.0000000
Syndig1l -6.604495 -1.274800 0.0000000 0.0000000
Gria1 -13.958590 -1.268362 0.0000000 0.0000000
Nptxr -13.889064 -1.262523 0.0000000 0.0000000
Vgf -12.293935 -1.258393 0.0000000 0.0000000
Cpne5 -5.260164 -1.241260 0.0000001 0.0000005
Enpp2 -6.956770 -1.240104 0.0000000 0.0000000
Olig1 -10.634375 -1.236012 0.0000000 0.0000000
Gpr158 -6.361823 -1.231967 0.0000000 0.0000000
Camk4 -10.088779 -1.231667 0.0000000 0.0000000
Trem2 -34.723385 -1.228153 0.0000000 0.0000000
Gria4 -4.943034 -1.218861 0.0000008 0.0000025
Lynx1 -15.970130 -1.214346 0.0000000 0.0000000
Rorb -5.016793 -1.211188 0.0000005 0.0000017
Rims2 -6.495607 -1.205873 0.0000000 0.0000000
Robo1 -7.861152 -1.190639 0.0000000 0.0000000
Erbb4 -2.753368 -1.188461 0.0058986 0.0133451
Dclk3 -7.753090 -1.175498 0.0000000 0.0000000
Prkce -6.479829 -1.164746 0.0000000 0.0000000
Epha7 -3.753278 -1.164692 0.0001745 0.0004875
Cd83 12.759947 1.162782 0.0000000 0.0000000
Drd2 -2.418683 -1.156987 0.0155768 0.0327244
Itga7 -2.342017 -1.146786 0.0191799 0.0396278
Cbs -3.463257 -1.146054 0.0005337 0.0013614
Myl9 -2.366356 -1.145835 0.0179641 0.0374253
Sst -6.153507 -1.141457 0.0000000 0.0000000
Apoe 26.440660 1.140031 0.0000000 0.0000000
Serpinf1 -5.001376 -1.128805 0.0000006 0.0000018
Gad2 -6.844688 -1.128761 0.0000000 0.0000000
Brinp1 -8.307802 -1.126785 0.0000000 0.0000000
App -31.694534 -1.118341 0.0000000 0.0000000
Rims1 -5.009360 -1.117869 0.0000005 0.0000018
Slc30a3 -4.545061 -1.117339 0.0000055 0.0000166
Gja1 -9.814078 -1.110382 0.0000000 0.0000000
Abi3 -28.741728 -1.104618 0.0000000 0.0000000
Pvalb -3.606583 -1.101951 0.0003103 0.0008296
Cck -7.808821 -1.096803 0.0000000 0.0000000
Slc17a7 -12.869619 -1.090657 0.0000000 0.0000000
Gad1 -6.309830 -1.090095 0.0000000 0.0000000
Pdgfrb 10.181975 1.087649 0.0000000 0.0000000
Cx3cl1 -12.226503 -1.080976 0.0000000 0.0000000
Nptx2 -3.165335 -1.080356 0.0015490 0.0036534
Chrm4 -2.562861 -1.075552 0.0103814 0.0225682
Spi1 -16.132265 -1.073453 0.0000000 0.0000000
Pcdhac2 -4.466461 -1.060731 0.0000080 0.0000240
Flt1 -3.773511 -1.048025 0.0001610 0.0004522
Cnr1 -3.087397 -1.028985 0.0020192 0.0046740
Ntrk2 -5.276340 -1.026675 0.0000001 0.0000004
Hs3st1 -3.338516 -1.024509 0.0008423 0.0020543
Arc -12.419890 -1.007726 0.0000000 0.0000000

4.15 MY_MB_P_HY Neuron

names scores logfoldchanges pvals pvals_adj
Car4 -4.436538 -1.380672 9.1e-06 2.1e-05
Adarb2 -8.519075 -1.119324 0.0e+00 0.0e+00
Trhr -5.851647 -1.103519 0.0e+00 0.0e+00
Npy1r -7.593289 -1.039569 0.0e+00 0.0e+00
Mapk1 -18.737139 -1.038007 0.0e+00 0.0e+00
Bmp2 -5.488219 -1.031323 0.0e+00 1.0e-07
Gabra1 -29.626926 -1.020203 0.0e+00 0.0e+00
Ndnf -5.255598 -1.003972 1.0e-07 4.0e-07

4.16 Oligo

names scores logfoldchanges pvals pvals_adj
Cd74 10.98096 2.915869 0 0
Serpina3n 11.48777 2.064526 0 0
C4b 22.08805 1.753775 0 0

4.17 OPC

names scores logfoldchanges pvals pvals_adj
Cd74 22.063580 5.299099 0.0000000 0.0000000
Cxcl10 4.022185 4.074791 0.0000577 0.0002300
C4b 28.681534 3.342240 0.0000000 0.0000000
Serpina3n 21.517027 3.116985 0.0000000 0.0000000
Ly9 5.846620 3.035228 0.0000000 0.0000000
Cst7 5.871054 2.952172 0.0000000 0.0000000
Clec7a 7.447059 2.937019 0.0000000 0.0000000
C3 5.330118 2.827415 0.0000001 0.0000005
Ctss 22.755754 2.662425 0.0000000 0.0000000
C1qa 10.651853 2.084364 0.0000000 0.0000000
Spp1 9.045135 1.947595 0.0000000 0.0000000
Atf3 3.494980 1.814261 0.0004741 0.0016932
Itgam 3.553034 1.801209 0.0003808 0.0013798
Lgals3 4.560864 1.729119 0.0000051 0.0000218
Inpp5d 6.757185 1.680977 0.0000000 0.0000000
Cspg5 -31.098356 -1.623373 0.0000000 0.0000000
Ctsc 2.822587 1.622701 0.0047638 0.0146128
Gfap 17.763878 1.505473 0.0000000 0.0000000
Trem2 3.999100 1.340515 0.0000636 0.0002503
Cldn11 12.248850 1.325029 0.0000000 0.0000000
Icam1 3.458820 1.303741 0.0005425 0.0019239
Egr1 -9.152687 -1.290269 0.0000000 0.0000000
Ptpru -16.821754 -1.281802 0.0000000 0.0000000
Rph3a -20.120094 -1.276112 0.0000000 0.0000000
Cspg4 -27.315598 -1.266995 0.0000000 0.0000000
Hpca -11.625162 -1.237670 0.0000000 0.0000000
Bcan -27.927422 -1.218149 0.0000000 0.0000000
Enpp6 3.793122 1.152743 0.0001488 0.0005551
Klk6 2.773283 1.132912 0.0055494 0.0168287
Adrb1 -3.040492 -1.126666 0.0023619 0.0076958
Cacng4 -24.494429 -1.126192 0.0000000 0.0000000
Pdgfra -22.711110 -1.126121 0.0000000 0.0000000
Olig1 -28.010956 -1.103647 0.0000000 0.0000000
Grm4 -5.235609 -1.084730 0.0000002 0.0000008
Syp -19.167921 -1.073679 0.0000000 0.0000000
Grin2b -7.905853 -1.073639 0.0000000 0.0000000
Rapgef3 -21.003948 -1.056739 0.0000000 0.0000000
Cdh9 -3.278109 -1.045031 0.0010450 0.0035306
Id4 -4.865310 -1.042507 0.0000011 0.0000051
Nefm -14.248327 -1.040641 0.0000000 0.0000000
Itgax 2.479415 1.003834 0.0131598 0.0378155
Scn4b -5.939970 -1.000151 0.0000000 0.0000000

4.18 Pericyte

names scores logfoldchanges pvals pvals_adj
Cd74 7.313498 2.096242 0.00e+00 0.0000000
C4b 4.340364 1.114589 1.42e-05 0.0001922

4.19 Pvalb GABA

names scores logfoldchanges pvals pvals_adj
Cd74 5.515627 2.760391 0.0e+00 3.0e-07
Egr1 -10.065308 -1.314686 0.0e+00 0.0e+00
Fos -6.761326 -1.251861 0.0e+00 0.0e+00
Lamp5 -4.470774 -1.025050 7.8e-06 5.9e-05
Adrb1 -6.606277 -1.004922 0.0e+00 0.0e+00

4.20 Sst GABA

names scores logfoldchanges pvals pvals_adj
Egr2 -3.166410 -2.114153 0.0015433 0.0065954
Cd74 3.100242 2.043140 0.0019336 0.0081245
Fos -10.758125 -1.968860 0.0000000 0.0000000
Egr1 -12.888699 -1.667493 0.0000000 0.0000000
Adrb1 -6.002086 -1.198177 0.0000000 0.0000000
Tpbg 5.189824 1.084485 0.0000002 0.0000015
Gfap 7.948716 1.002401 0.0000000 0.0000000

4.21 STR Neuron

names scores logfoldchanges pvals pvals_adj
Egr2 -15.252028 -2.046400 0.0000000 0.0000000
Wnt2 -22.535799 -1.943914 0.0000000 0.0000000
Htr2c -8.654650 -1.461609 0.0000000 0.0000000
Egr4 -26.267267 -1.341182 0.0000000 0.0000000
Sox8 -38.576256 -1.340200 0.0000000 0.0000000
Fosl2 -14.712869 -1.325358 0.0000000 0.0000000
Nnat -16.401468 -1.313548 0.0000000 0.0000000
Otof -18.600405 -1.291863 0.0000000 0.0000000
Id4 -31.579699 -1.215291 0.0000000 0.0000000
Cspg5 -41.360348 -1.206559 0.0000000 0.0000000
Ccnb2 -2.707878 -1.177844 0.0067715 0.0158850
Dlk1 -3.762596 -1.176348 0.0001682 0.0004645
Gfap 16.617020 1.154274 0.0000000 0.0000000
Fos -11.743439 -1.145487 0.0000000 0.0000000
Gpr63 -13.070436 -1.135917 0.0000000 0.0000000
Ntng1 -8.895514 -1.107336 0.0000000 0.0000000
Ndufa4l2 -3.067918 -1.092639 0.0021556 0.0052067
Cd74 4.845804 1.081961 0.0000013 0.0000038
Rasgrf2 -11.626558 -1.081005 0.0000000 0.0000000
Adrb1 -22.502580 -1.062318 0.0000000 0.0000000
Nr4a1 -24.893328 -1.061485 0.0000000 0.0000000
Fosb -11.564626 -1.019287 0.0000000 0.0000000
Npy1r -7.798757 -1.017111 0.0000000 0.0000000
Ccdc153 -2.605158 -1.014229 0.0091832 0.0208709
Grm3 -33.070084 -1.006981 0.0000000 0.0000000

4.22 SUB Glut

names scores logfoldchanges pvals pvals_adj
Cxcl10 3.855326 4.024214 0.0001156 0.0009473
Cd74 4.258404 3.719672 0.0000206 0.0001906
Htr1a -3.803162 -3.447729 0.0001429 0.0010823
Gad1 -2.816806 -3.217809 0.0048504 0.0247468
Egr4 -5.289810 -2.702437 0.0000001 0.0000019
Bcan -6.475335 -2.625699 0.0000000 0.0000000
Cspg5 -6.355596 -2.352687 0.0000000 0.0000000
Gpr37 -2.579701 -2.341383 0.0098886 0.0462083
Tpbg -3.053911 -2.287496 0.0022588 0.0129816
Ctss 4.740912 2.169066 0.0000021 0.0000236
C1qa 2.935358 2.073810 0.0033316 0.0183056
Fosb -2.698254 -2.061518 0.0069704 0.0331925
Fam131a -8.391142 -2.048522 0.0000000 0.0000000
Vgf -9.370385 -2.025132 0.0000000 0.0000000
C4b 2.750417 2.013255 0.0059520 0.0288930
Olig1 -2.591556 -1.979323 0.0095543 0.0450674
Sst -3.525750 -1.951085 0.0004223 0.0028924
Kcnh7 -5.180742 -1.930994 0.0000002 0.0000028
Elfn1 -6.406574 -1.904427 0.0000000 0.0000000
Adrb1 -3.920529 -1.868130 0.0000884 0.0007617
Syp -8.678039 -1.829211 0.0000000 0.0000000
Scn4b -5.714228 -1.776210 0.0000000 0.0000002
Kcnab1 -6.031949 -1.767018 0.0000000 0.0000000
Lratd2 -3.723732 -1.738506 0.0001963 0.0014225
Gabra1 -5.424960 -1.712346 0.0000001 0.0000009
Eno2 -8.003475 -1.697508 0.0000000 0.0000000
Prkce -3.668013 -1.684378 0.0002444 0.0017214
Hpca -7.758072 -1.658655 0.0000000 0.0000000
Grm4 -4.445717 -1.655440 0.0000088 0.0000912
Sox8 -3.815018 -1.639205 0.0001362 0.0010475
Gja1 -4.972089 -1.628194 0.0000007 0.0000077
Dkk3 -7.084694 -1.619981 0.0000000 0.0000000
Nrg3 -6.066329 -1.596105 0.0000000 0.0000000
Pde11a -3.160608 -1.574169 0.0015744 0.0091535
Fos -3.703578 -1.558526 0.0002126 0.0015184
Psen2 -2.940101 -1.551981 0.0032811 0.0182281
Dlg4 -7.803122 -1.534408 0.0000000 0.0000000
Htr5a -2.870155 -1.533630 0.0041027 0.0217557
Egr1 -6.263125 -1.514333 0.0000000 0.0000000
Ppp1r1b -5.257801 -1.482707 0.0000001 0.0000020
Chrm4 -3.980991 -1.481933 0.0000686 0.0006020
Nefm -7.404786 -1.449955 0.0000000 0.0000000
Gria1 -7.134486 -1.440787 0.0000000 0.0000000
Grin2a -5.995197 -1.427760 0.0000000 0.0000000
Rph3a -6.456366 -1.427725 0.0000000 0.0000000
Hrh3 -2.750417 -1.419643 0.0059520 0.0288930
Neurod6 -3.378745 -1.418038 0.0007282 0.0046678
Gpr158 -3.618221 -1.399720 0.0002966 0.0020600
Syn1 -7.023047 -1.381249 0.0000000 0.0000000
Cx3cl1 -7.363292 -1.371256 0.0000000 0.0000000
Kcnd2 -3.212771 -1.339038 0.0013146 0.0078251
Cnr1 -2.925874 -1.324338 0.0034349 0.0186679
Arc -5.805513 -1.315159 0.0000000 0.0000001
Grb2 -4.343761 -1.315120 0.0000140 0.0001401
Ntng2 -2.867783 -1.310559 0.0041336 0.0217557
Cplx1 -7.255410 -1.309365 0.0000000 0.0000000
Ddit3 3.407197 1.301511 0.0006563 0.0043180
Rbfox3 -6.050917 -1.288186 0.0000000 0.0000000
Grin2b -6.105451 -1.286515 0.0000000 0.0000000
Syngap1 -6.641308 -1.284447 0.0000000 0.0000000
Gfap 4.339019 1.263877 0.0000143 0.0001403
Tbr1 -2.560733 -1.220888 0.0104452 0.0483572
Epha10 -3.845841 -1.175429 0.0001201 0.0009628
Fn1 -3.276790 -1.170132 0.0010499 0.0064811
Fosl2 -5.055076 -1.153369 0.0000004 0.0000052
Nr4a2 -6.242972 -1.152081 0.0000000 0.0000000
Camk2a -5.261357 -1.151298 0.0000001 0.0000020
Crhr1 -3.843470 -1.106770 0.0001213 0.0009628
Neto1 -5.511503 -1.106329 0.0000000 0.0000006
Slc17a7 -6.110193 -1.094327 0.0000000 0.0000000
Csf1r 2.968553 1.092889 0.0029921 0.0168093
Hcn1 -5.014769 -1.082623 0.0000005 0.0000063
Pdgfa -3.983362 -1.080629 0.0000679 0.0006020
Lynx1 -5.211565 -1.076340 0.0000002 0.0000025
Epha7 -3.883778 -1.069280 0.0001028 0.0008570
Ptpru -3.733217 -1.051279 0.0001890 0.0013901
Cck -4.272630 -1.050309 0.0000193 0.0001822
App -7.203247 -1.046736 0.0000000 0.0000000
Grm2 -3.475958 -1.034469 0.0005090 0.0034394
Fezf2 -5.066931 -1.014270 0.0000004 0.0000051

4.23 TH Neuron

names scores logfoldchanges pvals pvals_adj
Cd74 20.283000 4.144462 0.0000000 0.0000000
Clec7a 5.017197 2.693154 0.0000005 0.0000021
Spp1 10.799181 2.535002 0.0000000 0.0000000
Ctss 18.911268 2.177782 0.0000000 0.0000000
C1qa 6.249269 1.654239 0.0000000 0.0000000
Gfap 19.100382 1.636467 0.0000000 0.0000000
Cox6a2 -5.455903 -1.534525 0.0000000 0.0000002
Bcan -16.649742 -1.328575 0.0000000 0.0000000
Itga7 -13.342796 -1.271336 0.0000000 0.0000000
C4b 3.158005 1.243737 0.0015885 0.0049333
Adrb1 -14.787244 -1.238746 0.0000000 0.0000000
Sox8 -4.416718 -1.233021 0.0000100 0.0000377
Cspg5 -16.573458 -1.187774 0.0000000 0.0000000
Inpp5d 2.972330 1.173289 0.0029555 0.0089021
C3 4.039569 1.165907 0.0000535 0.0001886
Ngf -6.835734 -1.160955 0.0000000 0.0000000
Htr5a -4.322067 -1.152700 0.0000155 0.0000564
Csf1r 7.813028 1.149611 0.0000000 0.0000000
Ntng2 -2.692629 -1.138832 0.0070891 0.0201395
Car4 -11.091613 -1.122126 0.0000000 0.0000000
Sorl1 -8.363807 -1.109907 0.0000000 0.0000000
Fosl2 -3.111117 -1.092463 0.0018638 0.0057525
Egr1 -14.975497 -1.051914 0.0000000 0.0000000
Prkce -9.713602 -1.046305 0.0000000 0.0000000
Grm4 -17.761087 -1.026480 0.0000000 0.0000000
Gpr63 -7.396331 -1.019211 0.0000000 0.0000000
Adarb2 -10.372215 -1.019042 0.0000000 0.0000000
Coch -6.796173 -1.017654 0.0000000 0.0000000
Fos -10.408340 -1.016051 0.0000000 0.0000000
Dkk3 -2.517688 -1.000801 0.0118128 0.0322754

4.24 Vip_Lamp5_Sncg GABA

names scores logfoldchanges pvals pvals_adj
Cd74 4.028603 2.287394 0.0000561 0.0002953
Arc -8.919403 -1.129473 0.0000000 0.0000000
Gfap 10.678942 1.117905 0.0000000 0.0000000
Gpr63 -4.094939 -1.112987 0.0000422 0.0002246
Bcan -5.627124 -1.053312 0.0000000 0.0000001
Cspg5 -12.678706 -1.041377 0.0000000 0.0000000
Crebbp -2.775224 -1.018875 0.0055164 0.0227949
Fos -5.714624 -1.010770 0.0000000 0.0000001

4.25 VLMC

names scores logfoldchanges pvals pvals_adj
C3 2.998382 2.311522 0.0027142 0.0242337
Nr4a1 -6.931097 -1.662902 0.0000000 0.0000000
Nr4a2 -4.254446 -1.545675 0.0000210 0.0003613
Egr1 -3.512555 -1.191276 0.0004438 0.0050434
Cd74 8.197221 1.154254 0.0000000 0.0000000
Hs3st1 -3.973159 -1.095896 0.0000709 0.0010430
Plagl1 -3.333734 -1.089891 0.0008569 0.0087437
Camk2a -3.939495 -1.044447 0.0000817 0.0011665
Npy1r -3.071756 -1.036848 0.0021280 0.0197041

Abbreviation

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic